Although bactericidal antibiotics are an integral part of infectious disease medicine, the uncontrolled use of these drugs in recent years is beginning to affect the environment, especially water resources. With the exception of a few well-documented toxic effects, antimicrobials are thought to act mainly on bacteria and, at low doses, have no deleterious effects on eukaryotic organisms. However, since mitochondria are direct ancient relatives of prokaryotes, mitochondrial dysfunction induced by antibiotic exposure can also occur in higher eukaryotes. In this work, we used the microcrustacean Artemia salina to show how some known antibacterial drugs exert toxic effects on mitochondria, suppressing cellular and organismal respiration in aquatic organisms. We have demonstrated that exposure to antimicrobials of different classes, namely kanamycin A, tetracycline hydrochloride, erythromycin, and chloramphenicol, leads to the accumulation of reactive oxygen species and is accompanied by autophagy. Our results suggest that the emergence of antibactericidal drugs, increasingly appearing in wastewater, may have far-reaching consequences for aquatic areas adjacent to large cities.